OMSSAXMLFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>

#include <vector>

namespace OpenMS
{
  class String;
  class ModificationsDB;

  class OPENMS_DLLAPI OMSSAXMLFile :
    protected Internal::XMLHandler,
    public Internal::XMLFile
  {
public:

    OMSSAXMLFile();

    ~OMSSAXMLFile() override;
    void load(const String& filename,
              ProteinIdentification& protein_identification,
              std::vector<PeptideIdentification>& id_data,
              bool load_proteins = true,
              bool load_empty_hits = true);

    void setModificationDefinitionsSet(const ModificationDefinitionsSet& rhs);

protected:
    // Docu in base class
    void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;

    // Docu in base class
    void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;

    // Docu in base class
    void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;

private:

    OMSSAXMLFile(const OMSSAXMLFile& rhs);

    OMSSAXMLFile& operator=(const OMSSAXMLFile& rhs);

    void readMappingFile_();

    std::vector<PeptideIdentification>* peptide_identifications_;

    ProteinHit actual_protein_hit_;

    PeptideHit actual_peptide_hit_;

    PeptideEvidence actual_peptide_evidence_;

    std::vector<PeptideEvidence> actual_peptide_evidences_;

    PeptideIdentification actual_peptide_id_;

    ProteinIdentification actual_protein_id_;

    String tag_;

    UInt actual_mod_site_;

    String actual_mod_type_;

    std::vector<std::pair<UInt, String> > modifications_;

    bool load_proteins_;

    bool load_empty_hits_;

    Map<UInt, std::vector<ResidueModification> > mods_map_;

    Map<String, UInt> mods_to_num_;

    ModificationDefinitionsSet mod_def_set_;
  };

} // namespace OpenMS